If you figure this one out, let me know! My Super Mario Bros. is doing the same thing. I took off the apron and found that the outhole kicker was kicking the drained Ball 1 too hard into the other balls. Ball 1 would bounce off the balls, go back through the gate, and hit the outhole switch again. Then it would get kicked back up the trough, hitting the balls again which would release the second ball.

I replaced the resistance spring in the outhole kicker thinking maybe that was bad, but still having problems. Going to try replacing the trough gate next because when the ball goes through it, sometimes it does not fall back down like it should to block the ball going backwards. Anyway, hope that helps!

All trough switches are working and the game registers 3 balls to start, but during play I would get this issue intermittently after a ball drains. Davebart set me on the right path though! I am going to try to press down the switch that the balls rest on to make sure it is not crooked and interfering with the balls at rest.

Glad I am not the only one having this problem too!